https://github.com/bioinfotongli/spatialdata
Spatial Data
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.7%) to scientific vocabulary
Last synced: 9 months ago
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JSON representation
Repository
Spatial Data
Basic Info
- Host: GitHub
- Owner: BioinfoTongLI
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Size: 2.09 MB
Statistics
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 0
Fork of scverse/spatialdata
Created over 3 years ago
· Last pushed over 1 year ago
https://github.com/BioinfoTongLI/spatialdata/blob/main/
 # SpatialData: an open and universal framework for processing spatial omics data. [![Tests][badge-tests]][link-tests] [](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main) [](https://codecov.io/gh/scverse/spatialdata) [](https://spatialdata.scverse.org/en/latest/) [](https://zenodo.org/badge/latestdoi/487366481) [](https://pepy.tech/project/spatialdata) [](https://github.com/scverse/spatialdata/actions/workflows/release.yaml) SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem. - [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata. - [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata. - [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data. [//]: # "numfocus-fiscal-sponsor-attribution" The spatialdata project uses a [consensus based governance model](https://scverse.org/about/roles/) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/). Consider making a [tax-deductible donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs. The spatialdata project also received support by the Chan Zuckerberg Initiative.
 - **The library is currently under review.** We expect there to be changes as the community provides feedback. We have an announcement channel for communicating these changes, please see the contact section below. - The SpatialData storage format is built on top of the [OME-NGFF](https://ngff.openmicroscopy.org/latest/) specification. ## Getting started Please refer to the [documentation][link-docs]. In particular: - [API documentation][link-api]. - [Design doc][link-design-doc]. - [Example notebooks][link-notebooks]. Another useful resource to get started is the source code of the [`spatialdata-io`](https://github.com/scverse/spatialdata-io) package, which shows example of how to read data from common technologies. ## Installation Check out the docs for more complete [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html). To get started with the "batteries included" installation, you can install via pip: ```bash pip install "spatialdata[extra]" ``` or via conda: ```bash mamba install -c conda-forge spatialdata napari-spatialdata spatialdata-io spatialdata-plot ``` ## Limitations - Code only manually tested for Windows machines. Currently the framework is being developed using Linux, macOS and Windows machines, but it is automatically tested only for Linux and macOS machines. ## Contact To get involved in the discussion, or if you need help to get started, you are welcome to use the following options. - Chat via [`scverse` Zulip](https://scverse.zulipchat.com/#narrow/stream/315824-spatial) (public or 1 to 1). - Forum post in the [scverse discourse forum](https://discourse.scverse.org/). - Bug report/feature request via the [GitHub issue tracker][issue-tracker]. - Zoom call as part of the SpatialData Community Meetings, held every 2 weeks on Thursday, [schedule here](https://hackmd.io/enWU826vRai-JYaL7TZaSw). Finally, especially relevant for for developers that are building a library upon `spatialdata`, please follow this channel for: - Announcements on new features and important changes [Zulip](https://imagesc.zulipchat.com/#narrow/stream/329057-scverse/topic/spatialdata.20announcements). ## Citation Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x [scverse-discourse]: https://discourse.scverse.org/ [issue-tracker]: https://github.com/scverse/spatialdata/issues [changelog]: https://spatialdata.readthedocs.io/latest/changelog.html [design doc]: https://scverse-spatialdata.readthedocs.io/en/latest/design_doc.html [link-docs]: https://spatialdata.scverse.org/en/latest/ [link-api]: https://spatialdata.scverse.org/en/latest/api.html [link-design-doc]: https://spatialdata.scverse.org/en/latest/design_doc.html [link-notebooks]: https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks.html [badge-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml/badge.svg [link-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml
Owner
- Name: Tong LI
- Login: BioinfoTongLI
- Kind: user
- Location: Hinxton
- Company: Wellcome Sanger Institute
- Repositories: 4
- Profile: https://github.com/BioinfoTongLI
GitHub Events
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- Push event: 8
Last Year
- Push event: 8